Improve python distribution

setup.py

@@ -7,37 +7,107 @@ def fatal_error(reason):
     sys.exit(1)
 
 if os.path.exists('CMakeLists.txt'):
-    fatal_error("The setup.py script should be executed from the build directory. Please see the file 'README.md' for further instructions.")
+    fatal_error("The setup.py script should be executed from the build directory. Please see the file 'README.md' for instructions.")
 
 if 'sdist' in sys.argv:
     fatal_error("This package contains precompiled extension modules, it cannot be distributed as a source package.")
 
+__version__ = open(os.path.join(os.path.dirname(__file__), 'src/VERSION')).read().strip()
+long_description = open(os.path.join(os.path.dirname(__file__), 'README.rst')).read()
 
-class BinaryDistribution(Distribution):
-    """Since we don't use distutils Extension mecanism for building the module
-    we have to fake it by overloading Distribution.
-    """
-    def has_ext_modules(self):
-        return True
+# We have to trick distutils into thinking that we have an "extension module"
+# even if it is not declared because we compile it our-self. This change the way
+# bdists, eggs, and wheels are emitted, by tagging them with a platform dependant
+# tag.
 
+# One part of the goal is to have Distribution.has_ext_modules() returning True
+# (which further implies that Distribution.is_pure() is False). This could be
+# accomplished with a simple shim :
+
+# class BinaryDistribution(Distribution):
+#     """Since we don't use distutils Extension mecanism for building the module
+#     we have to fake it by overloading Distribution.
+#     """
+#     def has_ext_modules(self):
+#         return True
+
+# Sadly this is not enough : some part of distutils bypasses has_ext_modules()
+# by testing the truth value of the ext_modules directly.
+
+# One solution would be patching Extension to skip the compilation passe, but
+# Extension is only a declarative interface : the actual compilation is made out
+# of the class in the build_ext command. This route could be further explored by
+# looking at how Cython manage to do this (it seems that it implements its own
+# build_ext)
+
+# For now, the simplest (but quite hackish) solution I came with is an empty
+# list that lies by telling that its length is 1 (implying a True truth value):
+
+class FakeNonEmptyList(list):
+    def __len__(self): return 1
 
 setup(
     # Package description
     name = "pyGATB",
-    version = '0.1',
+    version = __version__,
     description = 'An experimental python wrapper for gatb-core',
-    keywords = 'gatb debruijn genomic assembly',
-    license = 'AGPL',
+    long_description = long_description,
+    keywords = 'gatb debruijn genomics assembly',
+    license = 'AGPLv3',
     author = 'gatb-tools team',
     author_email = 'gatb-tools-support@lists.gforge.inria.fr',
     url = 'https://gatb.inria.fr/',
+    classifiers=[
+        # Topic
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.',
+        'Topic :: Scientific/Engineering :: Information Analysis',
+        'Topic :: Scientific/Engineering :: Visualization',
+        'Topic :: Software Development :: Libraries :: Application Frameworks',
+        'Topic :: Software Development :: Libraries :: Python Modules',
+
+        # Audience
+        'Intended Audience :: Science/Research',
+        'Intended Audience :: Developers',
+        'Intended Audience :: Healthcare Industry',
+        'Intended Audience :: Education',
+
+        'License :: OSI Approved :: GNU Affero General Public License v3',
+
+        # How mature is this project? Common values are
+        #   3 - Alpha
+        #   4 - Beta
+        #   5 - Production/Stable
+        'Development Status :: 3 - Alpha',
+
+        # Environnement, OS, languages
+        'Environment :: Console',
+
+        'Operating System :: MacOS :: MacOS X',
+        'Operating System :: POSIX :: Linux',
+        'Operating System :: POSIX',
+
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: Implementation :: CPython',
+        'Programming Language :: C++',
+        'Programming Language :: Cython',
+    ],
+
     # Package content
     packages=['gatb', 'gatb.tests'],
     package_dir = {'gatb': 'src'},
-    package_data = {'gatb': ['*.so'], 'gatb.tests': ['db/*']},
-    #eager_resources=['*.so'],
-    distclass=BinaryDistribution,
-    zip_safe = False,
+    package_data = {'gatb': ['core.so', 'VERSION'],
+                    'gatb.tests': ['db/*']
+                    },
+    data_files = [('', ['LICENSE'])],
+
+    #distclass=BinaryDistribution,
+    #ext_modules = [Extension('test', ['test.c'])],
+    ext_modules = FakeNonEmptyList(),
+
     # Runtime dependencies
     setup_requires = ['pytest-runner'] if {'pytest', 'test', 'ptr'}.intersection(sys.argv) else [],
     tests_require = ['pytest'],

src/VERSION

@@ -0,0 +1 @@
+0.1a0

src/__init__.py

@@ -1,2 +1,13 @@
+"""
+Two main gatb-core API are exposed in python :
+    * Graph: for constructing and loading gatb graph
+    * Bank: for loading sequences from FASTA, FASTAQ, and text file defining collections.
+"""
+__all__ = ['Bank', 'Graph']
+
+import os
+
 # Import public facing API for re-export
 from .core import Bank, Graph
+
+__version__ = open(os.path.join(os.path.dirname(__file__), 'VERSION')).read().strip()